labfreed 0.2.7__py3-none-any.whl → 0.2.8__py3-none-any.whl

labfreed/__init__.py

@@ -1,11 +1,11 @@
-''' 
-Python implementation of LabFREED building blocks
-'''
-
-__version__ = "0.2.7"
-
-from labfreed.pac_id import *  # noqa: F403
-from labfreed.pac_cat import * # noqa: F403
-from labfreed.pac_id_resolver import * # noqa: F403
-from labfreed.trex import * # noqa: F403
-from labfreed.labfreed_infrastructure import *  # noqa: F403
+''' 
+Python implementation of LabFREED building blocks
+'''
+
+__version__ = "0.2.8"
+
+from labfreed.pac_id import *  # noqa: F403
+from labfreed.pac_cat import * # noqa: F403
+from labfreed.pac_id_resolver import * # noqa: F403
+from labfreed.trex import * # noqa: F403
+from labfreed.labfreed_infrastructure import *  # noqa: F403

labfreed/labfreed_infrastructure.py

@@ -1,258 +1,258 @@
-from enum import Enum, auto
-import logging
-import re
-from pydantic import BaseModel, ConfigDict, Field, PrivateAttr, field_validator
-from typing import Any, List, Set
-
-from rich import print
-from rich.table import Table
-
-''' Configure pdoc'''
-__all__ = ["LabFREED_BaseModel", "ValidationMessage", "ValidationMsgLevel", "LabFREED_ValidationError"]
-
-class PDOC_Workaround_Base(BaseModel):
-    '''@private
-    This class only exists to make pdoc work better with Pydantic models. It is set up such, that some things are not showing up in docu
-    '''
-    model_config = ConfigDict(extra="forbid")
-    """@private"""
-    def model_post_init(self, context: Any) -> None:
-        '''@private'''
-        super().model_post_init(context)
-
-
-
-
-
-class ValidationMsgLevel(Enum):
-    '''
-    Level of validation messages
-    '''
-    ERROR = auto() 
-    '''Model is **invalid**'''
-    WARNING = auto() 
-    '''Model is **valid**, but has issues'''
-    RECOMMENDATION = auto()
-    '''Model is **valid**, but recommendations apply'''
-    INFO = auto()
-    '''Model is **valid**. Something of interest was detected, which is not a recommendation.'''
-
-class ValidationMessage(PDOC_Workaround_Base):
-    '''
-    Represents one problem in the model
-    '''
-    source_id:int
-    source:str 
-    level: ValidationMsgLevel
-    msg:str
-    highlight:str = "" #this can be used to highlight problematic parts
-    highlight_sub_patterns:list[str] = Field(default_factory=list)
-
-    @field_validator('highlight_sub_patterns', mode='before')
-    @classmethod
-    def _ensure_list(cls, v):
-        if isinstance(v, str):
-            return [v]
-        return v
-
-
-    
-class LabFREED_ValidationError(ValueError):
-    '''Error which is raised, when LabFREED validation fails, i.e. when the model contains at least one error.'''
-    
-    def __init__(self, message=None, validation_msgs=None):
-        '''@private'''
-        super().__init__(message)
-        self._validation_msgs = validation_msgs
-
-    @property
-    def validation_msgs(self):
-        ''' The validation messages (errors, recommendations, info) present in the invalid model'''
-        return self._validation_msgs
-    
-    
-
-
-class LabFREED_BaseModel(PDOC_Workaround_Base):
-    """ Extension of Pydantic BaseModel, so that validator can issue warnings.
-    The purpose of that is to allow only minimal validation but on top check for stricter recommendations"""
-    
-    _validation_messages: list[ValidationMessage] = PrivateAttr(default_factory=list)
-    """Validation messages for this model"""
-    
-    @property
-    def is_valid(self) -> bool:
-        return len(self.errors()) == 0
-    
-
-    def validation_messages(self, nested=True) -> list[ValidationMessage]:
-        if nested:
-            msgs = self._get_nested_validation_messages()
-        else:
-            msgs = self._validation_messages
-        return msgs
-    
-    def errors(self, nested=True) -> list[ValidationMessage]: 
-        return _filter_errors(self.validation_messages(nested=nested))
-    
-    def warnings(self, nested=True) -> list[ValidationMessage]: 
-        return _filter_warnings(self.validation_messages(nested=nested))
-    
-
-    def _add_validation_message(self, *, msg: str, level:ValidationMsgLevel, source:str="", highlight_pattern="", highlight_sub=None):
-        if not highlight_sub:
-            highlight_sub = []
-        w = ValidationMessage(msg=msg, source=source, level=level, highlight=highlight_pattern, highlight_sub_patterns=highlight_sub, source_id=id(self))
-
-        if w not in self._validation_messages:
-            self._validation_messages.append(w)
-
-    # Function to extract warnings from a model and its nested models
-    def _get_nested_validation_messages(self, parent_name: str = "", visited: Set[int] = None) -> List['ValidationMessage']:
-        """
-        Recursively extract warnings from a Pydantic model and its nested fields, including computed fields.
-
-        :param parent_name: The name of the parent model to track the path.
-        :param visited: Set of visited object IDs to prevent infinite loops.
-        :return: List of ValidationMessages from this and nested models.
-        """
-        if visited is None:
-            visited = set()
-
-        model_id = id(self)
-        if model_id in visited:
-            return []
-        visited.add(model_id)
-
-        warnings_list = [warning for warning in self.validation_messages(nested=False)]
-
-        # Traverse regular fields
-        for field_name, field in self.__fields__.items():
-            full_path = f"{parent_name}.{field_name}" if parent_name else field_name
-            value = getattr(self, field_name)
-
-            if isinstance(value, LabFREED_BaseModel):
-                warnings_list.extend(value._get_nested_validation_messages(full_path, visited))
-            elif isinstance(value, list):
-                for index, item in enumerate(value):
-                    if isinstance(item, LabFREED_BaseModel):
-                        list_path = f"{full_path}[{index}]"
-                        warnings_list.extend(item._get_nested_validation_messages(list_path, visited))
-
-        # Traverse computed fields
-        computed_fields = getattr(self, '__pydantic_decorators__', {}).computed_fields or {}
-        for field_name in computed_fields:
-            full_path = f"{parent_name}.{field_name}" if parent_name else field_name
-            try:
-                value = getattr(self, field_name)
-            except Exception:
-                continue  # Safely skip computed properties that raise errors
-
-            if isinstance(value, LabFREED_BaseModel):
-                warnings_list.extend(value._get_nested_validation_messages(full_path, visited))
-            elif isinstance(value, list):
-                for index, item in enumerate(value):
-                    if isinstance(item, LabFREED_BaseModel):
-                        list_path = f"{full_path}[{index}]"
-                        warnings_list.extend(item._get_nested_validation_messages(list_path, visited))
-
-        return warnings_list
-        
-
-    
-    def print_validation_messages(self, target='console'):
-        msgs = self.format_validation_messages(target=target)
-        
-        table = Table(title="Validation Results", show_header=False, title_justify='left')
-
-        def col(s):
-            return table.add_column(s, vertical='top')
-        col("-")
-        
-        if not msgs:
-            table.add_row('All clear!', end_section=True)
-            return
-
-        for m in msgs:
-            table.add_row(m)
-            table.add_section()
-
-        logging.info(table)
-        print(table)
-        return table
-        
-        
-    def format_validation_messages(self, target='console') -> list[str]:
-        """Format validation messages
-
-        Args:
-            target (str, optional): Target format: 'markdown', 'console', 'html', 'html_styled'.
-
-        Returns:
-            list[str]: formated messages
-        """
-        formatted_msg = list()
-        for m in self.validation_messages():
-            if m.level == ValidationMsgLevel.ERROR:
-                color = '#d70000'
-            else:
-                color = '#d78700'
-                
-            match target:
-                case 'markdown':
-                    fmt = lambda s: f'👉{s}👈'  # noqa: E731
-                    fmt_title = lambda s: f'**{s}**'  # noqa: E731
-                    br = '\n'
-                case 'console':     
-                    fmt = lambda s: f'[{color} bold]{s}[/{color} bold]'  # noqa: E731
-                    fmt_title = fmt
-                    br = '\n'
-                case 'html':
-                    lvl = m.level.name.lower()
-                    fmt = lambda s: f'<span class="validation-problem {lvl}">{s}</span>'  # noqa: E731
-                    fmt_title = lambda s: f'<span class="validation-title {lvl}">{s}</span>'  # noqa: E731
-                    br = '<br>'
-                case 'html_styled':
-                    fmt = lambda s: f'<b style="color:{color}">{s}</b>'  # noqa: E731
-                    fmt_title = fmt
-                    br = '<br>'
-                
-            serialized = str(self)
-            serialized = serialized.replace('\n', br)
-            emphazised_highlight = self._emphasize_in(m, serialized, fmt=fmt)
-            emphazised_highlight = emphazised_highlight.replace('👈👉','') # removes two consecutive markers, to make it cleaner
-            
-            txt =   f'{fmt_title(m.level.name)} in {m.source}'
-            txt += br + f'{m.msg}'
-            txt += br+br + emphazised_highlight
-            
-            formatted_msg.append(txt)
-        return formatted_msg
-    
-    def _emphasize_in(self, validation_msg, validation_node_str:str, fmt):
-        if validation_msg.highlight_sub_patterns:
-            replacements = validation_msg.highlight_sub_patterns
-        else:
-            replacements = [validation_msg.highlight]
-        # Sort patterns by length descending to avoid subpattern clobbering
-        sorted_patterns = sorted(replacements, key=len, reverse=True)
-        # Escape the patterns for regex safety
-        escaped_patterns = [re.escape(p) for p in sorted_patterns]
-        # Create one regex pattern with alternation (longest first)
-        pattern = re.compile("|".join(escaped_patterns))
-        
-        out = pattern.sub(lambda m: fmt(m.group(0)), validation_node_str)
-        return out
-            
-
-    
-def _filter_errors(val_msg:list[ValidationMessage]) -> list[ValidationMessage]:
-    return [ m for m in val_msg if m.level == ValidationMsgLevel.ERROR ]
-
-def _filter_warnings(val_msg:list[ValidationMessage]) -> list[ValidationMessage]:
-    return [ m for m in val_msg if m.level != ValidationMsgLevel.ERROR  ]     
-
-def _quote_texts(texts:list[str]):
-    return ','.join([f"'{t}'" for t in texts])
-
-
+from enum import Enum, auto
+import logging
+import re
+from pydantic import BaseModel, ConfigDict, Field, PrivateAttr, field_validator
+from typing import Any, List, Set
+
+from rich import print
+from rich.table import Table
+
+''' Configure pdoc'''
+__all__ = ["LabFREED_BaseModel", "ValidationMessage", "ValidationMsgLevel", "LabFREED_ValidationError"]
+
+class PDOC_Workaround_Base(BaseModel):
+    '''@private
+    This class only exists to make pdoc work better with Pydantic models. It is set up such, that some things are not showing up in docu
+    '''
+    model_config = ConfigDict(extra="forbid")
+    """@private"""
+    def model_post_init(self, context: Any) -> None:
+        '''@private'''
+        super().model_post_init(context)
+
+
+
+
+
+class ValidationMsgLevel(Enum):
+    '''
+    Level of validation messages
+    '''
+    ERROR = auto() 
+    '''Model is **invalid**'''
+    WARNING = auto() 
+    '''Model is **valid**, but has issues'''
+    RECOMMENDATION = auto()
+    '''Model is **valid**, but recommendations apply'''
+    INFO = auto()
+    '''Model is **valid**. Something of interest was detected, which is not a recommendation.'''
+
+class ValidationMessage(PDOC_Workaround_Base):
+    '''
+    Represents one problem in the model
+    '''
+    source_id:int
+    source:str 
+    level: ValidationMsgLevel
+    msg:str
+    highlight:str = "" #this can be used to highlight problematic parts
+    highlight_sub_patterns:list[str] = Field(default_factory=list)
+
+    @field_validator('highlight_sub_patterns', mode='before')
+    @classmethod
+    def _ensure_list(cls, v):
+        if isinstance(v, str):
+            return [v]
+        return v
+
+
+    
+class LabFREED_ValidationError(ValueError):
+    '''Error which is raised, when LabFREED validation fails, i.e. when the model contains at least one error.'''
+    
+    def __init__(self, message=None, validation_msgs=None):
+        '''@private'''
+        super().__init__(message)
+        self._validation_msgs = validation_msgs
+
+    @property
+    def validation_msgs(self):
+        ''' The validation messages (errors, recommendations, info) present in the invalid model'''
+        return self._validation_msgs
+    
+    
+
+
+class LabFREED_BaseModel(PDOC_Workaround_Base):
+    """ Extension of Pydantic BaseModel, so that validator can issue warnings.
+    The purpose of that is to allow only minimal validation but on top check for stricter recommendations"""
+    
+    _validation_messages: list[ValidationMessage] = PrivateAttr(default_factory=list)
+    """Validation messages for this model"""
+    
+    @property
+    def is_valid(self) -> bool:
+        return len(self.errors()) == 0
+    
+
+    def validation_messages(self, nested=True) -> list[ValidationMessage]:
+        if nested:
+            msgs = self._get_nested_validation_messages()
+        else:
+            msgs = self._validation_messages
+        return msgs
+    
+    def errors(self, nested=True) -> list[ValidationMessage]: 
+        return _filter_errors(self.validation_messages(nested=nested))
+    
+    def warnings(self, nested=True) -> list[ValidationMessage]: 
+        return _filter_warnings(self.validation_messages(nested=nested))
+    
+
+    def _add_validation_message(self, *, msg: str, level:ValidationMsgLevel, source:str="", highlight_pattern="", highlight_sub=None):
+        if not highlight_sub:
+            highlight_sub = []
+        w = ValidationMessage(msg=msg, source=source, level=level, highlight=highlight_pattern, highlight_sub_patterns=highlight_sub, source_id=id(self))
+
+        if w not in self._validation_messages:
+            self._validation_messages.append(w)
+
+    # Function to extract warnings from a model and its nested models
+    def _get_nested_validation_messages(self, parent_name: str = "", visited: Set[int] = None) -> List['ValidationMessage']:
+        """
+        Recursively extract warnings from a Pydantic model and its nested fields, including computed fields.
+
+        :param parent_name: The name of the parent model to track the path.
+        :param visited: Set of visited object IDs to prevent infinite loops.
+        :return: List of ValidationMessages from this and nested models.
+        """
+        if visited is None:
+            visited = set()
+
+        model_id = id(self)
+        if model_id in visited:
+            return []
+        visited.add(model_id)
+
+        warnings_list = [warning for warning in self.validation_messages(nested=False)]
+
+        # Traverse regular fields
+        for field_name, field in self.__fields__.items():
+            full_path = f"{parent_name}.{field_name}" if parent_name else field_name
+            value = getattr(self, field_name)
+
+            if isinstance(value, LabFREED_BaseModel):
+                warnings_list.extend(value._get_nested_validation_messages(full_path, visited))
+            elif isinstance(value, list):
+                for index, item in enumerate(value):
+                    if isinstance(item, LabFREED_BaseModel):
+                        list_path = f"{full_path}[{index}]"
+                        warnings_list.extend(item._get_nested_validation_messages(list_path, visited))
+
+        # Traverse computed fields
+        computed_fields = getattr(self, '__pydantic_decorators__', {}).computed_fields or {}
+        for field_name in computed_fields:
+            full_path = f"{parent_name}.{field_name}" if parent_name else field_name
+            try:
+                value = getattr(self, field_name)
+            except Exception:
+                continue  # Safely skip computed properties that raise errors
+
+            if isinstance(value, LabFREED_BaseModel):
+                warnings_list.extend(value._get_nested_validation_messages(full_path, visited))
+            elif isinstance(value, list):
+                for index, item in enumerate(value):
+                    if isinstance(item, LabFREED_BaseModel):
+                        list_path = f"{full_path}[{index}]"
+                        warnings_list.extend(item._get_nested_validation_messages(list_path, visited))
+
+        return warnings_list
+        
+
+    
+    def print_validation_messages(self, target='console'):
+        msgs = self.format_validation_messages(target=target)
+        
+        table = Table(title="Validation Results", show_header=False, title_justify='left')
+
+        def col(s):
+            return table.add_column(s, vertical='top')
+        col("-")
+        
+        if not msgs:
+            table.add_row('All clear!', end_section=True)
+            return
+
+        for m in msgs:
+            table.add_row(m)
+            table.add_section()
+
+        logging.info(table)
+        print(table)
+        return table
+        
+        
+    def format_validation_messages(self, target='console') -> list[str]:
+        """Format validation messages
+
+        Args:
+            target (str, optional): Target format: 'markdown', 'console', 'html', 'html_styled'.
+
+        Returns:
+            list[str]: formated messages
+        """
+        formatted_msg = list()
+        for m in self.validation_messages():
+            if m.level == ValidationMsgLevel.ERROR:
+                color = '#d70000'
+            else:
+                color = '#d78700'
+                
+            match target:
+                case 'markdown':
+                    fmt = lambda s: f'👉{s}👈'  # noqa: E731
+                    fmt_title = lambda s: f'**{s}**'  # noqa: E731
+                    br = '\n'
+                case 'console':     
+                    fmt = lambda s: f'[{color} bold]{s}[/{color} bold]'  # noqa: E731
+                    fmt_title = fmt
+                    br = '\n'
+                case 'html':
+                    lvl = m.level.name.lower()
+                    fmt = lambda s: f'<span class="validation-problem {lvl}">{s}</span>'  # noqa: E731
+                    fmt_title = lambda s: f'<span class="validation-title {lvl}">{s}</span>'  # noqa: E731
+                    br = '<br>'
+                case 'html_styled':
+                    fmt = lambda s: f'<b style="color:{color}">{s}</b>'  # noqa: E731
+                    fmt_title = fmt
+                    br = '<br>'
+                
+            serialized = str(self)
+            serialized = serialized.replace('\n', br)
+            emphazised_highlight = self._emphasize_in(m, serialized, fmt=fmt)
+            emphazised_highlight = emphazised_highlight.replace('👈👉','') # removes two consecutive markers, to make it cleaner
+            
+            txt =   f'{fmt_title(m.level.name)} in {m.source}'
+            txt += br + f'{m.msg}'
+            txt += br+br + emphazised_highlight
+            
+            formatted_msg.append(txt)
+        return formatted_msg
+    
+    def _emphasize_in(self, validation_msg, validation_node_str:str, fmt):
+        if validation_msg.highlight_sub_patterns:
+            replacements = validation_msg.highlight_sub_patterns
+        else:
+            replacements = [validation_msg.highlight]
+        # Sort patterns by length descending to avoid subpattern clobbering
+        sorted_patterns = sorted(replacements, key=len, reverse=True)
+        # Escape the patterns for regex safety
+        escaped_patterns = [re.escape(p) for p in sorted_patterns]
+        # Create one regex pattern with alternation (longest first)
+        pattern = re.compile("|".join(escaped_patterns))
+        
+        out = pattern.sub(lambda m: fmt(m.group(0)), validation_node_str)
+        return out
+            
+
+    
+def _filter_errors(val_msg:list[ValidationMessage]) -> list[ValidationMessage]:
+    return [ m for m in val_msg if m.level == ValidationMsgLevel.ERROR ]
+
+def _filter_warnings(val_msg:list[ValidationMessage]) -> list[ValidationMessage]:
+    return [ m for m in val_msg if m.level != ValidationMsgLevel.ERROR  ]     
+
+def _quote_texts(texts:list[str]):
+    return ','.join([f"'{t}'" for t in texts])
+
+

labfreed/pac_cat/__init__.py

@@ -1,20 +1,20 @@
-from .pac_cat import PAC_CAT
-from .category_base import Category
-from .predefined_categories import (
-    Material_Device, Material_Substance, Material_Consumable, Material_Misc, Data_Method, Data_Result, Data_Progress, 
-    Data_Calibration, Data_Abstract, category_key_to_class_map  # noqa: F401
-    )
-
-__all__ = [
-    "PAC_CAT",
-    "Category",
-    "Material_Device",
-    "Material_Substance",
-    "Material_Consumable",
-    "Material_Misc",
-    "Data_Method",
-    "Data_Result",
-    "Data_Progress",
-    "Data_Calibration",
-    "Data_Abstract"
+from .pac_cat import PAC_CAT
+from .category_base import Category
+from .predefined_categories import (
+    Material_Device, Material_Substance, Material_Consumable, Material_Misc, Data_Method, Data_Result, Data_Progress, 
+    Data_Calibration, Data_Abstract, category_key_to_class_map  # noqa: F401
+    )
+
+__all__ = [
+    "PAC_CAT",
+    "Category",
+    "Material_Device",
+    "Material_Substance",
+    "Material_Consumable",
+    "Material_Misc",
+    "Data_Method",
+    "Data_Result",
+    "Data_Progress",
+    "Data_Calibration",
+    "Data_Abstract"
 ]